Experts and Doctors on x ray crystallography in Denmark


Locale: Denmark
Topic: x ray crystallography

Top Publications

  1. Kristiansen M, Andersen B, Iversen L, Westergaard N. Identification, synthesis, and characterization of new glycogen phosphorylase inhibitors binding to the allosteric AMP site. J Med Chem. 2004;47:3537-45 pubmed
    ..This compound together with a closely related analogue was further characterized by enzyme kinetics and in primary rat hepatocytes. ..
  2. Yde C, Ermakova I, Issinger O, Niefind K. Inclining the purine base binding plane in protein kinase CK2 by exchanging the flanking side-chains generates a preference for ATP as a cosubstrate. J Mol Biol. 2005;347:399-414 pubmed
    ..These findings demonstrate that CK2alpha possesses sophisticated structural adaptations in favour of dual-cosubstrate specificity, suggesting that this property could be of biological significance. ..
  3. Babavali M, Esmann M, Fedosova N, Marsh D. Urea-induced unfolding of Na,K-ATPase as evaluated by electron paramagnetic resonance spectroscopy. Biochemistry. 2009;48:9022-30 pubmed publisher
    ..Susceptibility of the latter could arise from the nonhomologous regions in the cytoplasmic domain...
  4. Bondensgaard K, Breinholt J, Madsen D, Omkvist D, Kang L, Worsaae A, et al. The existence of multiple conformers of interleukin-21 directs engineering of a superpotent analogue. J Biol Chem. 2007;282:23326-36 pubmed
    ..An hIL-21 analog was designed to stabilize the region around helix C through the introduction of a segment grafted from hIL-4. This novel hIL-21 analog was demonstrated to exhibit a 10-fold increase in potency in a cellular assay. ..
  5. Windahl M, Petersen C, Christensen H, Harris P. Crystal structure of tryptophan hydroxylase with bound amino acid substrate. Biochemistry. 2008;47:12087-94 pubmed publisher
    ..In fact, the chicken TPH1.Trp.imidazole structure resembles the PAH.BH 4.thienylalanine structure more (root-mean-square deviation for Calpha atoms of 0.90 A) than the human TPH1 structure (root-mean-square deviation of 1.47 A). ..
  6. Johansson E, Bjornberg O, Nyman P, Larsen S. Structure of the bifunctional dCTP deaminase-dUTPase from Methanocaldococcus jannaschii and its relation to other homotrimeric dUTPases. J Biol Chem. 2003;278:27916-22 pubmed publisher
    ..The active site contains two water molecules that are engaged in hydrogen bonds to the invariant residues Ser118, Arg122, Thr130, and Glu145. These water molecules are potential nucleophile candidates in the deamination reaction...
  7. Morth J, Pedersen B, Toustrup Jensen M, Sørensen T, Petersen J, Andersen J, et al. Crystal structure of the sodium-potassium pump. Nature. 2007;450:1043-9 pubmed
    ..The carboxy terminus of the alpha-subunit is contained within a pocket between transmembrane helices and seems to be a novel regulatory element controlling sodium affinity, possibly influenced by the membrane potential. ..
  8. Hansen M, Le Nours J, Johansson E, Antal T, Ullrich A, Löffler M, et al. Inhibitor binding in a class 2 dihydroorotate dehydrogenase causes variations in the membrane-associated N-terminal domain. Protein Sci. 2004;13:1031-42 pubmed
  9. Pedersen L, Henriksen A. Expression, purification and crystallization of two peroxisomal acyl-CoA oxidases from Arabidopsis thaliana. Acta Crystallogr D Biol Crystallogr. 2004;60:1125-8 pubmed
    ..A selenomethionine-substituted form of the protein was produced and two-wavelength MAD data were collected at beamline BW7A, EMBL Outstation, Hamburg. ..

More Information

Publications112 found, 100 shown here

  1. Sørensen T, Møller J, Nissen P. Phosphoryl transfer and calcium ion occlusion in the calcium pump. Science. 2004;304:1672-5 pubmed
    ..The conformational changes that accompany the reaction with ATP pull the transmembrane helices 1 and 2 and close a cytosolic entrance for Ca2+, thereby preventing backflow before Ca2+ is released on the other side of the membrane. ..
  2. Gad H, Dellgren C, Hamming O, Vends S, Paludan S, Hartmann R. Interferon-lambda is functionally an interferon but structurally related to the interleukin-10 family. J Biol Chem. 2009;284:20869-75 pubmed publisher
    ..In particular, we found an interesting similarity between IFN-lambda and IL-22, and we suggest that IFN-lambda and IL-22 possess parallel functions, protecting epithelial tissue against viral and bacterial infections, respectively. ..
  3. McDonough M, Kadirvelraj R, Harris P, Poulsen J, Larsen S. Rhamnogalacturonan lyase reveals a unique three-domain modular structure for polysaccharide lyase family 4. FEBS Lett. 2004;565:188-94 pubmed
    ..The 508-amino acid polypeptide displays a unique arrangement of three distinct modular domains. Each domain shows structural homology to non-catalytic domains from other carbohydrate active enzymes. ..
  4. Lo Leggio L, Dal Degan F, Poulsen P, Andersen S, Larsen S. The structure and specificity of Escherichia coli maltose acetyltransferase give new insight into the LacA family of acyltransferases. Biochemistry. 2003;42:5225-35 pubmed
    ..Structural differences at the acceptor site reflect the differences in substrate specificity. ..
  5. Kristensen O, Ross B, Gajhede M. Structure of the PPX/GPPA phosphatase from Aquifex aeolicus in complex with the alarmone ppGpp. J Mol Biol. 2008;375:1469-76 pubmed publisher
    ..The arginines R22 and R267, residing in different domains, are crucial for guanosine pentaphosphate specificity as they interact with the unique 3'-ribose phosphorylation...
  6. Andersen K, Jonstrup A, Van L, Brodersen D. The activity and selectivity of fission yeast Pop2p are affected by a high affinity for Zn2+ and Mn2+ in the active site. RNA. 2009;15:850-61 pubmed publisher
    ..Finally, we use site-directed mutagenesis to propose a mechanistic model for the basis of the preference for poly-A sequences exhibited by the Pop2p-type deadenylases as well as their distributive enzymatic behavior. ..
  7. He Y, Andersen G, Nielsen K. Structural basis for the function of DEAH helicases. EMBO Rep. 2010;11:180-6 pubmed publisher
    ..The structure of Prp43p provides the framework for functional and genetic analysis of all DEAH helicases. ..
  8. Sauerberg P, Pettersson I, Jeppesen L, Bury P, Mogensen J, Wassermann K, et al. Novel tricyclic-alpha-alkyloxyphenylpropionic acids: dual PPARalpha/gamma agonists with hypolipidemic and antidiabetic activity. J Med Chem. 2002;45:789-804 pubmed
    ..Investigations of the pharmacokinetics of selected compounds suggested that extended drug exposure improved the in vivo activity of in vitro active compounds. ..
  9. Jørgensen R, Ortiz P, Carr Schmid A, Nissen P, Kinzy T, Andersen G. Two crystal structures demonstrate large conformational changes in the eukaryotic ribosomal translocase. Nat Struct Biol. 2003;10:379-85 pubmed
    ..The two structures also emphasize the dynamic nature of the ribosomal translocase. ..
  10. Fredslund F, Laursen N, Roversi P, Jenner L, Oliveira C, Pedersen J, et al. Structure of and influence of a tick complement inhibitor on human complement component 5. Nat Immunol. 2008;9:753-60 pubmed publisher
    ..The structure of C5 may render possible a structure-based approach for the design of new selective complement inhibitors. ..
  11. Valnickova Z, Sanglas L, Arolas J, Petersen S, Schar C, Otzen D, et al. Flexibility of the thrombin-activatable fibrinolysis inhibitor pro-domain enables productive binding of protein substrates. J Biol Chem. 2010;285:38243-50 pubmed publisher
    ..This underlines the unusually flexible nature of the pro-domain and implies a possible mechanism for regulation of TAFI intrinsic proteolytic activity in vivo. ..
  12. Schack V, Morth J, Toustrup Jensen M, Anthonisen A, Nissen P, Andersen J, et al. Identification and function of a cytoplasmic K+ site of the Na+, K+ -ATPase. J Biol Chem. 2008;283:27982-90 pubmed publisher
  13. Brodersen D, Nyborg J, Kjeldgaard M. Zinc-binding site of an S100 protein revealed. Two crystal structures of Ca2+-bound human psoriasin (S100A7) in the Zn2+-loaded and Zn2+-free states. Biochemistry. 1999;38:1695-704 pubmed
    ..The structure of S100A7 crystallized in the absence of zinc further shows that loss of zinc results in a reorganization of the adjacent empty and distorted EF-hand loop, causing it to resemble a calcium-loaded EF-hand. ..
  14. Høg S, Wellendorph P, Nielsen B, Frydenvang K, Dahl I, Brauner Osborne H, et al. Novel high-affinity and selective biaromatic 4-substituted gamma-hydroxybutyric acid (GHB) analogues as GHB ligands: design, synthesis, and binding studies. J Med Chem. 2008;51:8088-95 pubmed publisher
    ..The affinity of the 4-[4'-(2-iodobenzyloxy)phenyl] GHB analogue 17b was shown to reside predominantly with the R-enantiomer (Ki = 22 nM), which has higher affinity than previously reported GHB ligands. ..
  15. Jensen M, Otten H, Christensen U, Borchert T, Christensen L, Larsen S, et al. Structural and biochemical studies elucidate the mechanism of rhamnogalacturonan lyase from Aspergillus aculeatus. J Mol Biol. 2010;404:100-11 pubmed publisher
    ..The mechanism differs significantly from the one established for pectate lyases, in which most often calcium ions are engaged in catalysis. ..
  16. Erichsen M, Huynh T, Abrahamsen B, Bastlund J, Bundgaard C, Monrad O, et al. Structure-activity relationship study of first selective inhibitor of excitatory amino acid transporter subtype 1: 2-Amino-4-(4-methoxyphenyl)-7-(naphthalen-1-yl)-5-oxo-5,6,7,8-tetrahydro-4H-chromene-3-carbonitrile (UCPH-101). J Med Chem. 2010;53:7180-91 pubmed publisher
    ..Finally, a bioavailability study of UCPH-101 determined the half-life to be 30 min in serum (rats) but also that it was not able to penetrate the blood-brain barrier to any significant degree. ..
  17. Rowland P, Bj rnberg O, Nielsen F, Jensen K, Larsen S. The crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A complexed with the enzyme reaction product throws light on its enzymatic function. Protein Sci. 1998;7:1269-79 pubmed publisher
  18. J rgensen R, Merrill A, Yates S, Marquez V, Schwan A, Boesen T, et al. Exotoxin A-eEF2 complex structure indicates ADP ribosylation by ribosome mimicry. Nature. 2005;436:979-84 pubmed publisher
    ..Notably, the toxin-bound betaTAD phosphates mimic the phosphate backbone of two nucleotides in a conformational switch of 18S rRNA, thereby achieving universal recognition of eEF2 by ETA...
  19. Mirza O, Skov L, Remaud Simeon M, Potocki de Montalk G, Albenne C, Monsan P, et al. Crystal structures of amylosucrase from Neisseria polysaccharea in complex with D-glucose and the active site mutant Glu328Gln in complex with the natural substrate sucrose. Biochemistry. 2001;40:9032-9 pubmed
    ..Both Asp394 and Arg446 are located in an insert connecting beta-strand 7 and alpha-helix 7 that is much longer in amylosucrase compared to other enzymes from the alpha-amylase family (family 13 of the glycoside hydrolases)...
  20. Andersen C, Anand M, Boesen T, Van L, Kinzy T, Andersen G. Purification and crystallization of the yeast translation elongation factor eEF3. Acta Crystallogr D Biol Crystallogr. 2004;60:1304-7 pubmed
    ..3 A. A density-modified map derived from low-resolution SIRAS phases allows model building. ..
  21. Celik L, Lund J, Schiøtt B. Conformational dynamics of the estrogen receptor alpha: molecular dynamics simulations of the influence of binding site structure on protein dynamics. Biochemistry. 2007;46:1743-58 pubmed
    ..Finally, the influence of such conformations on the biological function of ERalpha is discussed in relationship to the interaction with selective estrogen receptor modulators and endocrine-disrupting compounds. ..
  22. Rasmussen K, Kulahin N, Kristensen O, Poulsen J, Sigurskjold B, Kastrup J, et al. Crystal structure of the Ig1 domain of the neural cell adhesion molecule NCAM2 displays domain swapping. J Mol Biol. 2008;382:1113-20 pubmed publisher
    ..Taken together, these observations suggest that beta-strand swapping could have a role in the molecular mechanism of homophilic binding for NCAM2. ..
  23. Poulsen H, Khandelia H, Morth J, Bublitz M, Mouritsen O, Egebjerg J, et al. Neurological disease mutations compromise a C-terminal ion pathway in the Na(+)/K(+)-ATPase. Nature. 2010;467:99-102 pubmed publisher
    ..A similar ion regulation is likely to apply to the H(+)/K(+)-ATPase and the Ca(2+)-ATPase...
  24. Olsen J, Kadziola A, von Wettstein Knowles P, Siggaard Andersen M, Larsen S. Structures of beta-ketoacyl-acyl carrier protein synthase I complexed with fatty acids elucidate its catalytic machinery. Structure. 2001;9:233-43 pubmed
    ..The acyl binding pockets of KAS I and KAS II are so similar that they alone cannot provide the basis for their differences in substrate specificity. ..
  25. Lund I, Andersen H, Iversen L, Olsen O, Møller K, Pedersen A, et al. Structure-based design of selective and potent inhibitors of protein-tyrosine phosphatase beta. J Biol Chem. 2004;279:24226-35 pubmed
    ..Therefore, we anticipate that this strategy, here applied to PTPbeta, in principle can be used in the design and development of selective inhibitors of many, if not most PTPs. ..
  26. Kjaergaard M, Gardsvoll H, Hirschberg D, Nielbo S, Mayasundari A, Peterson C, et al. Solution structure of recombinant somatomedin B domain from vitronectin produced in Pichia pastoris. Protein Sci. 2007;16:1934-45 pubmed
    ..The NMR structure was determined for free SMB produced by Pichia and is largely consistent with that solved by X-ray crystallography for SMB in complex with PAI-1. ..
  27. Cabrera S, Reyes E, Alemán J, Milelli A, Kobbelgaard S, Jørgensen K. Organocatalytic asymmetric synthesis of alpha,alpha-disubstituted alpha-amino acids and derivatives. J Am Chem Soc. 2008;130:12031-7 pubmed publisher
  28. Rasmussen H, Branner S, Wiberg F, Wagtmann N. Crystal structure of human dipeptidyl peptidase IV/CD26 in complex with a substrate analog. Nat Struct Biol. 2003;10:19-25 pubmed
    ..Both domains participate in inhibitor binding. The structure indicates how substrate specificity is achieved and reveals a new and unexpected opening to the active site. ..
  29. Jeppesen M, Navratil T, Spremulli L, Nyborg J. Crystal structure of the bovine mitochondrial elongation factor Tu.Ts complex. J Biol Chem. 2005;280:5071-81 pubmed
    ..The structure of the EF-Tumt.Tsmt complex provides new insights into the nucleotide exchange mechanism and provides a framework for explaining much of the mutational data obtained for this complex. ..
  30. Kirkensgaard K, Hägglund P, Finnie C, Svensson B, Henriksen A. Structure of Hordeum vulgare NADPH-dependent thioredoxin reductase 2. Unwinding the reaction mechanism. Acta Crystallogr D Biol Crystallogr. 2009;65:932-41 pubmed publisher
    ..Here, analysis of interdomain contacts as well as phylogenetic studies lead to the proposal of a new reaction scheme in which NTR-Trx interactions mediate the FO to FR transformation. ..
  31. Kadziola A, Neuhard J, Larsen S. Structure of product-bound Bacillus caldolyticus uracil phosphoribosyltransferase confirms ordered sequential substrate binding. Acta Crystallogr D Biol Crystallogr. 2002;58:936-45 pubmed
    ..This is consistent with kinetic data, which display ordered sequential binding of substrates, with PRPP binding first. Based on this observation, a reaction mechanism is proposed. ..
  32. Cramer J, Gustafsen C, Behrens M, Oliveira C, Pedersen J, Madsen P, et al. GGA autoinhibition revisited. Traffic. 2010;11:259-73 pubmed publisher
    ..Taken together, our findings seem to refute the functional significance of GGA autoinhibition in particular and of intrinsic GGA binding motifs in general. ..
  33. Fiorentini M, Nielsen A, Kristensen O, Kastrup J, Gajhede M. Structure of the first PDZ domain of human PSD-93. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009;65:1254-7 pubmed publisher
    ..However, the cleft is significantly narrower in PSD-95. This could be part of the basis of peptide selectivity between PSD-93 PDZ1 and PSD-95 PDZ1. ..
  34. Tidow H, Hein K, Baekgaard L, Palmgren M, Nissen P. Expression, purification, crystallization and preliminary X-ray analysis of calmodulin in complex with the regulatory domain of the plasma-membrane Ca2+-ATPase ACA8. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66:361-3 pubmed publisher
    ..8, b = 70.0, c = 69.8 A, beta = 113.2 degrees. A complete data set was collected to 3.0 A resolution and structure determination is in progress in order to elucidate the mechanism of PMCA activation by calmodulin. ..
  35. Boesen T, Mohammad S, Pavitt G, Andersen G. Structure of the catalytic fragment of translation initiation factor 2B and identification of a critically important catalytic residue. J Biol Chem. 2004;279:10584-92 pubmed
  36. Ernst H, Willemoes M, Lo Leggio L, Leonard G, Blum P, Larsen S. Characterization of different crystal forms of the alpha-glucosidase MalA from Sulfolobus solfataricus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005;61:1039-42 pubmed
    ..5 A resolution have been collected. Self-rotation functions calculated for this form and for the orthorhombic (P2(1)2(1)2(1)) form 2 indicate the presence of six molecules in the asymmetric unit related by 32 symmetry. ..
  37. N rager S, Jensen K, Bj rnberg O, Larsen S. E. coli dihydroorotate dehydrogenase reveals structural and functional distinctions between different classes of dihydroorotate dehydrogenases. Structure. 2002;10:1211-23 pubmed
    ..Significant differences between the two classes of DHODs were identified by comparison of the E. coli DHOD with the other known DHOD structures, and differences with the class 2 human DHOD explain the variation in their inhibitors...
  38. Ebdrup S, Pettersson I, Rasmussen H, Deussen H, Frost Jensen A, Mortensen S, et al. Synthesis and biological and structural characterization of the dual-acting peroxisome proliferator-activated receptor alpha/gamma agonist ragaglitazar. J Med Chem. 2003;46:1306-17 pubmed
  39. Vogensen S, Frydenvang K, Greenwood J, Postorino G, Nielsen B, Pickering D, et al. A tetrazolyl-substituted subtype-selective AMPA receptor agonist. J Med Chem. 2007;50:2408-14 pubmed
  40. Bernardi L, López Cantarero J, Niess B, Jørgensen K. Organocatalytic asymmetric 1,6-additions of beta-ketoesters and glycine imine. J Am Chem Soc. 2007;129:5772-8 pubmed
    ..The synthetic utility of this asymmetric reaction is demonstrated by the two-step transformation of the allylated alpha-amino acid derivative to highly attractive optically active pyrrolidines. ..
  41. Pedersen B, Morth J, Nissen P. Structure determination using poorly diffracting membrane-protein crystals: the H+-ATPase and Na+,K+-ATPase case history. Acta Crystallogr D Biol Crystallogr. 2010;66:309-13 pubmed publisher
    ..This approach has been used in the structure determination of H(+)-ATPase and Na(+),K(+)-ATPase using Ca(2+)-ATPase models and its successful application to the Mhp1 symporter using LeuT as a search model is demonstrated. ..
  42. Bukrinsky J, St Hilaire P, Meldal M, Crocker P, Henriksen A. Complex of sialoadhesin with a glycopeptide ligand. Biochim Biophys Acta. 2004;1702:173-9 pubmed
    ..The structure of the glycopeptide complex suggests strategies for ligand optimization and provides possible explanations for the observed differences in specificities among the Siglecs. ..
  43. Parmeggiani A, Krab I, Watanabe T, Nielsen R, Dahlberg C, Nyborg J, et al. Enacyloxin IIa pinpoints a binding pocket of elongation factor Tu for development of novel antibiotics. J Biol Chem. 2006;281:2893-900 pubmed
    ..This work clarifies the structural background of the action of enacyloxin IIa and compares its properties with those of kirromycin, opening new perspectives for structure-guided design of novel antibiotics. ..
  44. Nissen P, Kjeldgaard M, Thirup S, Polekhina G, Reshetnikova L, Clark B, et al. Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Science. 1995;270:1464-72 pubmed
    ..The overall shape of the ternary complex is similar to that of the translocation factor, EF-G-GDP, and this suggests a novel mechanism involving "molecular mimicry" in the translational apparatus. ..
  45. Vestergaard B, Van L, Andersen G, Nyborg J, Buckingham R, Kjeldgaard M. Bacterial polypeptide release factor RF2 is structurally distinct from eukaryotic eRF1. Mol Cell. 2001;8:1375-82 pubmed
  46. Soroka V, Kolkova K, Kastrup J, Diederichs K, Breed J, Kiselyov V, et al. Structure and interactions of NCAM Ig1-2-3 suggest a novel zipper mechanism for homophilic adhesion. Structure. 2003;11:1291-301 pubmed
    ..This arrangement results in two perpendicular zippers forming a double zipper-like NCAM adhesion complex. ..
  47. Nielsen M, Harris P, Ooi B, Christensen H. The 1.5 A resolution crystal structure of [Fe3S4]-ferredoxin from the hyperthermophilic archaeon Pyrococcus furiosus. Biochemistry. 2004;43:5188-94 pubmed publisher
    ..The crystal packing reveals a beta-sheet interaction, which supports the suggestion that P. furiosus ferredoxin is a functional dimer. The extraordinary thermostability of P. furiosus ferredoxin is further discussed...
  48. Kadziola A, Jepsen C, Johansson E, McGuire J, Larsen S, Hove Jensen B. Novel class III phosphoribosyl diphosphate synthase: structure and properties of the tetrameric, phosphate-activated, non-allosterically inhibited enzyme from Methanocaldococcus jannaschii. J Mol Biol. 2005;354:815-28 pubmed publisher
  49. Andersen C, Becker T, Blau M, Anand M, Halic M, Balar B, et al. Structure of eEF3 and the mechanism of transfer RNA release from the E-site. Nature. 2006;443:663-8 pubmed
    ..eEF3 uses an entirely new factor binding site near the ribosomal E-site, with the chromodomain likely to stabilize the ribosomal L1 stalk in an open conformation, thus allowing tRNA release. ..
  50. Nielsen J, B ggild A, Andersen C, Nielsen G, Boysen A, Brodersen D, et al. An Hfq-like protein in archaea: crystal structure and functional characterization of the Sm protein from Methanococcus jannaschii. RNA. 2007;13:2213-23 pubmed publisher
    ..Functional analysis reveals that Escherichia coli and M. jannaschii Hfqs display very similar biochemical and biological properties. It thus appears that the archaeal and bacterial Hfq proteins are largely functionally interchangeable...
  51. Alstrup Lie M, Schiøtt B. A DFT study of solvation effects on the tautomeric equilibrium and catalytic ylide generation of thiamin models. J Comput Chem. 2008;29:1037-47 pubmed
    ..Furthermore, inclusion of two water molecules to model the apoenzymatic environment lowers the activation energies of both direct and water-mediated ylide generation. ..
  52. Welinder K, Jørgensen M. Covalent structures of potato tuber lipases (patatins) and implications for vacuolar import. J Biol Chem. 2009;284:9764-9 pubmed publisher
    ..F. (2003) Biochemistry 42, 6696-6708), which included this propeptide thus, for the first time, shows the structure of a putative ligand of the vacuolar sorting receptor and processing enzyme responsible for patatin import. ..
  53. Bøgestrand S, Wiborg O, Thirup S, Nyborg J. Analysis and crystallization of a 25 kDa C-terminal fragment of cloned elongation factor Ts from Escherichia coli. FEBS Lett. 1995;368:49-54 pubmed
    ..The diffraction pattern shows a pronounced pseudo-C2 symmetry at low resolution. This pseudo symmetry increases when the crystals are irradiated with X-rays for a few hours. ..
  54. Poulsen J, Harris P, Jensen K, Larsen S. Selenomethionine substitution of orotidine-5'-monophosphate decarboxylase causes a change in crystal contacts and space group. Acta Crystallogr D Biol Crystallogr. 2001;57:1251-9 pubmed
    ..The change in space group appears to originate in differences in the crystal contacts near the SeMet and Met residues. These differences can be rationalized in terms of SeMet's larger size and hydrophobicity. ..
  55. Harris P, Poulsen J, Jensen K, Larsen S. Substrate binding induces domain movements in orotidine 5'-monophosphate decarboxylase. J Mol Biol. 2002;318:1019-29 pubmed
    ..The domain movements seem to be initiated by the phosphoryl binding to the enzyme and can explain why the binding of the phosphoryl group is essential for the catalytic function. ..
  56. Toustrup Jensen M, Vilsen B. Interaction between the catalytic site and the A-M3 linker stabilizes E2/E2P conformational states of Na+,K+-ATPase. J Biol Chem. 2005;280:10210-8 pubmed
  57. Kasper C, Pickering D, Mirza O, Olsen L, Kristensen A, Greenwood J, et al. The structure of a mixed GluR2 ligand-binding core dimer in complex with (S)-glutamate and the antagonist (S)-NS1209. J Mol Biol. 2006;357:1184-201 pubmed
    ..The displacement of (S)-glutamate by all antagonists was shown to be driven by enthalpy. ..
  58. Andersen C, Ballut L, Johansen J, Chamieh H, Nielsen K, Oliveira C, et al. Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA. Science. 2006;313:1968-72 pubmed
    ..The MAGOH and Y14 subunits lock eIF4AIII in a prehydrolysis state, and activation of the ATPase probably requires only modest conformational changes in eIF4AIII motif I. ..
  59. Runge S, Thøgersen H, Madsen K, Lau J, Rudolph R. Crystal structure of the ligand-bound glucagon-like peptide-1 receptor extracellular domain. J Biol Chem. 2008;283:11340-7 pubmed publisher
    ..The structure provides for the first time detailed molecular insight into ligand binding of the human GLP-1 receptor, an established target for treatment of type 2 diabetes. ..
  60. Micheelsen P, V vodov J, De Maria L, Ostergaard P, Friis E, Wilson K, et al. Structural and mutational analyses of the interaction between the barley alpha-amylase/subtilisin inhibitor and the subtilisin savinase reveal a novel mode of inhibition. J Mol Biol. 2008;380:681-90 pubmed publisher
    ..Mutational analysis showed that Thr88 is crucial for the inhibition, as it stabilises the interacting loop through intramolecular interactions with the BASI backbone...
  61. Meldal M, Tornøe C. Cu-catalyzed azide-alkyne cycloaddition. Chem Rev. 2008;108:2952-3015 pubmed publisher
  62. Hakansson K. The structure of Mg-ATPase nucleotide-binding domain at 1.6 A resolution reveals a unique ATP-binding motif. Acta Crystallogr D Biol Crystallogr. 2009;65:1181-6 pubmed publisher
    ..This motif consists of a short polypeptide stretch running very close to the ATP-binding site, while in Ca-ATPase the binding site is more open, with the corresponding polypeptide segment folded away from the active site. ..
  63. Kjeldgaard M, Nissen P, Thirup S, Nyborg J. The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation. Structure. 1993;1:35-50 pubmed
    ..GTP binding by EF-Tu leads to dramatic conformational changes which expose the tRNA binding site. It appears that tRNA binding to EF-Tu induces a further conformational change, which may affect the GTPase activity...
  64. Henriksen A, Aghajari N, Jensen K, Gajhede M. A flexible loop at the dimer interface is a part of the active site of the adjacent monomer of Escherichia coli orotate phosphoribosyltransferase. Biochemistry. 1996;35:3803-9 pubmed
    ..coli OPRTase are found in the substrate binding regions: the 5'-phosphate binding region (residues 120-131), the binding region for the orotate part of OMP (residues 25-27), and the pyrophosphate binding region (residues 71-73). ..
  65. Bentsen A, Larsen T, Kadziola A, Larsen S, Harlow K. Overexpression of Bacillus subtilis phosphoribosylpyrophosphate synthetase and crystallization and preliminary X-ray characterization of the free enzyme and its substrate-effector complexes. Proteins. 1996;24:238-46 pubmed
    ..The availability of the different complexes should allow questions regarding the molecular mechanisms of catalysis and allostery in PRPP synthetase to be addressed. ..
  66. Nissen P, Thirup S, Kjeldgaard M, Nyborg J. The crystal structure of Cys-tRNACys-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA. Structure. 1999;7:143-56 pubmed
    ..The structure of the 'kissing complex' shows a quasicontinuous helix with a distinct shape determined by the number of base pairs...
  67. Iversen L, Moller K, Pedersen A, Peters G, Petersen A, Andersen H, et al. Structure determination of T cell protein-tyrosine phosphatase. J Biol Chem. 2002;277:19982-90 pubmed
    ..Importantly, despite the high degree of functional and structural similarity between TC-PTP and PTP1B, we have been able to identify areas close to the active site that might be addressed to develop selective inhibitors of each enzyme. ..
  68. Karring H, Andersen G, Thirup S, Nyborg J, Spremulli L, Clark B. Isolation, crystallisation, and preliminary X-ray analysis of the bovine mitochondrial EF-Tu:GDP and EF-Tu:EF-Ts complexes. Biochim Biophys Acta. 2002;1601:172-7 pubmed
    ..78 A, c=128.89 A and beta=96.978 degrees. The crystals of the homologous mitochondrial EF-Tu:EF-Ts complex diffract to 4 A and belong to space group C2 with cell parameters a=157.7 A, b=151.9 A, c=156.9 A, and beta=108.96 degrees. ..
  69. Sprog e D, van den Broek L, Mirza O, Kastrup J, Voragen A, Gajhede M, et al. Crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis. Biochemistry. 2004;43:1156-62 pubmed publisher
    ..This results in a large cavity in the dimer, including the entrance to the two active sites...
  70. Valentin Hansen P, Eriksen M, Udesen C. The bacterial Sm-like protein Hfq: a key player in RNA transactions. Mol Microbiol. 2004;51:1525-33 pubmed
    ..Here, we summarize the history of Hfq and highlight results that have led to an important gain in insight into the physiology, biochemistry and evolution of Hfq and its homologues. ..
  71. Johansson E, Neuhard J, Willemoes M, Larsen S. Structural, kinetic, and mutational studies of the zinc ion environment in tetrameric cytidine deaminase. Biochemistry. 2004;43:6020-9 pubmed
    ..On the basis of the structures of R56A, R56Q, and C53H/R56Q an explanation is provided of kinetic results and the apparent instability of C53H/R56Q. ..
  72. Bjelke J, Christensen J, Branner S, Wagtmann N, Olsen C, Kanstrup A, et al. Tyrosine 547 constitutes an essential part of the catalytic mechanism of dipeptidyl peptidase IV. J Biol Chem. 2004;279:34691-7 pubmed
  73. H kansson K, Brugna M, Tasse L. The three-dimensional structure of catalase from Enterococcus faecalis. Acta Crystallogr D Biol Crystallogr. 2004;60:1374-80 pubmed publisher
    ..mirabilis. The solvent structure in the active site is identical in the four subunits but differs from that found in other catalases. The structural consequences of the Ramachandran outlier Ser196 are discussed...
  74. Skov L, Seppälä U, Coen J, Crickmore N, King T, Monsalve R, et al. Structure of recombinant Ves v 2 at 2.0 Angstrom resolution: structural analysis of an allergenic hyaluronidase from wasp venom. Acta Crystallogr D Biol Crystallogr. 2006;62:595-604 pubmed
    ..The analysis suggests that the harboured allergic IgE-mediated cross-reactivity between Ves v 2 and the allergen from D. maculata is much higher than that between Ves v 2 and the allergen from A. mellifera. ..
  75. Andersen C, Madsen M, Storm T, Moestrup S, Andersen G. Structural basis for receptor recognition of vitamin-B(12)-intrinsic factor complexes. Nature. 2010;464:445-8 pubmed publisher
  76. Arent S, Christensen C, Pye V, Nørgaard A, Henriksen A. The multifunctional protein in peroxisomal beta-oxidation: structure and substrate specificity of the Arabidopsis thaliana protein MFP2. J Biol Chem. 2010;285:24066-77 pubmed publisher
    ..Remarkably, neither of the two was able to catabolize enoyl-CoA substrates longer than 14 carbon atoms efficiently, suggesting the existence of an uncharacterized long chain enoyl-CoA hydratase in Arabidopsis peroxisomes. ..
  77. Vester Christensen M, Abou Hachem M, Svensson B, Henriksen A. Crystal structure of an essential enzyme in seed starch degradation: barley limit dextrinase in complex with cyclodextrins. J Mol Biol. 2010;403:739-50 pubmed publisher
    ..The crystal structures additionally provide new insight into cation sites and the concerted action of the battery of hydrolytic enzymes in starch degradation...
  78. Rowland P, Nielsen F, Jensen K, Larsen S. The crystal structure of the flavin containing enzyme dihydroorotate dehydrogenase A from Lactococcus lactis. Structure. 1997;5:239-52 pubmed
    ..The location of the conserved residues surrounding this cavity suggests the potential orientation of the substrate. ..
  79. Eriksen T, Kadziola A, Bentsen A, Harlow K, Larsen S. Structural basis for the function of Bacillus subtilis phosphoribosyl-pyrophosphate synthetase. Nat Struct Biol. 2000;7:303-8 pubmed
    ..In addition to identifying residues important for binding substrates and effectors, the structures suggest a novel mode of allosteric regulation. ..
  80. Peters G, Iversen L, Branner S, Andersen H, Mortensen S, Olsen O, et al. Residue 259 is a key determinant of substrate specificity of protein-tyrosine phosphatases 1B and alpha. J Biol Chem. 2000;275:18201-9 pubmed
    ..Both effects may indicate that PTPalpha regulates highly selective signal transduction processes. ..
  81. Holm M, Naur P, Vestergaard B, Geballe M, Gajhede M, Kastrup J, et al. A binding site tyrosine shapes desensitization kinetics and agonist potency at GluR2. A mutagenic, kinetic, and crystallographic study. J Biol Chem. 2005;280:35469-76 pubmed
  82. Jensen M, Mouritsen O. Single-channel water permeabilities of Escherichia coli aquaporins AqpZ and GlpF. Biophys J. 2006;90:2270-84 pubmed
    ..Consequently, suppressed water-water correlations across the narrow selectivity filter become a key structural determinant for water permeation causing luminal water to permeate slower across AqpZ. ..
  83. Fredslund F, Jenner L, Husted L, Nyborg J, Andersen G, Sottrup Jensen L. The structure of bovine complement component 3 reveals the basis for thioester function. J Mol Biol. 2006;361:115-27 pubmed
    ..Structure-based design of inhibitors of C3 activation may target a conserved pocket between the alpha-chain and the beta-chain of C3, which appears essential for conformational changes in C3. ..
  84. Hakansson K, Østergaard H, Winther J. Crystallization of mutant forms of glutaredoxin Grx1p from yeast. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006;62:920-2 pubmed
    ..0 A (synchrotron radiation) and 2.7 A (rotating-anode generator), respectively. In contrast, rxYFP-Grx1p formed crystals at high pH in MgSO(4) which diffract synchrotron radiation to 2.7 A. ..
  85. Jonstrup A, Andersen K, Van L, Brodersen D. The 1.4-A crystal structure of the S. pombe Pop2p deadenylase subunit unveils the configuration of an active enzyme. Nucleic Acids Res. 2007;35:3153-64 pubmed
  86. Maerten E, Cabrera S, Kjaersgaard A, Jørgensen K. Organocatalytic asymmetric direct phosphonylation of alpha,beta-unsaturated aldehydes: mechanism, scope, and application in synthesis. J Org Chem. 2007;72:8893-903 pubmed
    ..DFT calculations have been applied to explain the approach of the phosphite to the reactive carbon atom in the iminium intermediate in order to account for the observed absolute enantioselectivity in the reaction...
  87. Nielsen M, Seo E, Bozonnet S, Aghajari N, Robert X, Haser R, et al. Multi-site substrate binding and interplay in barley alpha-amylase 1. FEBS Lett. 2008;582:2567-71 pubmed publisher
    ..Additional delicate structure/function relationships of the secondary site are uncovered using Y380A/H395A, Y380A, and H395A AMY1 mutants. ..
  88. Underwood C, Garibay P, Knudsen L, Hastrup S, Peters G, Rudolph R, et al. Crystal structure of glucagon-like peptide-1 in complex with the extracellular domain of the glucagon-like peptide-1 receptor. J Biol Chem. 2010;285:723-30 pubmed publisher
    ..The data support the existence of differences in the binding modes of GLP-1 and exendin-4 on the full-length GLP-1 receptor. ..
  89. Kidmose R, Vasiliev N, Chetverin A, Andersen G, Knudsen C. Structure of the Qbeta replicase, an RNA-dependent RNA polymerase consisting of viral and host proteins. Proc Natl Acad Sci U S A. 2010;107:10884-9 pubmed publisher
    ..The evolution of resistance by the host appears to be impaired because of the interactions of the beta-subunit with parts of EF-Tu essential in recognition of aminoacyl-tRNA...
  90. Winther A, Liu H, Sonntag Y, Olesen C, le Maire M, Soehoel H, et al. Critical roles of hydrophobicity and orientation of side chains for inactivation of sarcoplasmic reticulum Ca2+-ATPase with thapsigargin and thapsigargin analogs. J Biol Chem. 2010;285:28883-92 pubmed publisher
    ..Finally, we propose that the Tg binding pocket may be a regulatory site that, for example, is sensitive to cholesterol. ..
  91. Nielsen F, Rowland P, Larsen S, Jensen K. Purification and characterization of dihydroorotate dehydrogenase A from Lactococcus lactis, crystallization and preliminary X-ray diffraction studies of the enzyme. Protein Sci. 1996;5:852-6 pubmed
    ..2%. Analysis of the solvent content and the self-rotation function indicates that the two subunits in the asymmetric unit are related by a noncrystallographic twofold axis perpendicular to the crystallographic b and c axes. ..
  92. Skov L, Mirza O, Sprogøe D, Dar I, Remaud Simeon M, Albenne C, et al. Oligosaccharide and sucrose complexes of amylosucrase. Structural implications for the polymerase activity. J Biol Chem. 2002;277:47741-7 pubmed
    ..The polymer binding introduces structural changes that allow sucrose to migrate from its binding site into the active site and displace the polymer. ..